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1dde

STRUCTURE OF THE DNAG CATALYTIC CORE

Method: X-RAY DIFFRACTION D_max: 78.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dde
deposition_date	1999-11-09
title	STRUCTURE OF THE DNAG CATALYTIC CORE
keywords	TOPRIM, 3-HELIX BUNDLE, DNA-BINDING PROTEIN, RNA POLYMERASE, REPLICATION PROTEIN, PRIMASE, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	23.19 Å
rg_electron	22.53 Å
i0	22309300.00
molecular_weight	35231.0 kDa
excluded_volume	43691 Å³
envelope_volume	51749 Å³
shell_volume	20387 Å³
envelope_diameter	82.6 Å
shell_rg	28.19 Å
envelope_rg	22.94 Å
shape_rg	22.55 Å
total_rg	23.17 Å
total_atoms	2460
n_residues	310
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	78.1 Å
rg_real	23.33 Å
rg_real_error	0.61 Å
i0_real	2.2310e+07
i0_real_error	3.3820e+05
rg_reciprocal	23.30 Å
i0_reciprocal	22310000.0000
total_estimate	0.7870
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.0 Å
skewness	0.550
kurtosis	-0.094
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	4835000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	DNA PRIMASE
formula_weight	38222.3 kDa
ec_number	2.7.7.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2750

MRGSHHHHHHGSGSMHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQLERLMPK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	YTTRIUM ION
formula_weight	88.9 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	290

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6. Citations (1)

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length_a	38.020 Å
length_b	55.890 Å
length_c	139.490 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.700 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2090
r_free	0.2630

fit	/app/data/saxs_computation/dd/1dde/1dde.fit
pddf	/app/data/pr_computation/dd/1dde/1dde.pr.out
profile	/app/data/saxs_computation/dd/1dde/1dde.dat

STRUCTURE OF THE DNAG CATALYTIC CORE

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction